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To view ongoing changes that haven't been finalized or merged yet, check our active pull-requests on GitHub

Enhancements

  • added OnOff, TimeProportional, and FuzzyLogic controllers, plus a StirringHotPlate device to lab_automation app, including an .eval() method and comprehensive documentation for sensors, controllers, and devices
  • added create_prebuild function to database.utils for creating date-stamped SQLite3 database archives
  • added the simmate dev command group with tools for linting, testing, and workspace management
  • improved CLI help texts and added rich markdown support across all command groups
  • update cas_registry app to use the official API as the primary backend and add a validation step to the chatbot lookup tool to verify cas
  • improved inventory_management by adding Molecule and Structure tables for detailed substance tracking, linking substances to all other datasets, and beginning to build data explorer views
  • added StructureInput and htmx_structure_input to standardize crystal structure loading across forms
  • updated the OQMD data loading method to support the latest data provided by their team
  • added draft of accuracy_rating to workflows to help beginners select the most appropriate settings
  • added a @schedule decorator for easier periodic task registration
  • added web components and templates for the pdb and chembl apps
  • added crystalline dataset views to the Data Explorer, including 3D structure views, exports, and search forms
  • added @batch_bulk_create decorator to help simplify load_source_data methods
  • updated simmate database download to be dynamic across all apps, support a --source option, and respect custom load orders
  • added first draft of vasp dockerfile. vasp is proprietary so source files and final image cannot be shared publicly
  • added methods for updating rows and cleaning up chunk files to toolkit datastore class
  • added parallel chunk loading to MoleculeStore datastores using UUID filenames, reorganize_chunks, and SLURM-compatible job submission via SimmateExecutor
  • established working helm chart for k3s single-node deployment
  • added web reports for static energy and relaxation calculations
  • added plotly data streaming
  • added base datastore class
  • prototyped usearch vector db
  • built out chemspace s3 datastore
  • upgraded qe and evolution apps
  • added qe sssp to docker images
  • enabled update-many selection
  • enabled updates for @batch_bulk_create decorator
  • added a fork of simple_pid
  • added an on keyword argument for weekly schedules

Refactors

  • moved simmate.workflows.execution and simmate.workflows.scheduler to simmate.compute to align with the CLI and documentation structure
  • renamed the simmate engine command group to simmate compute and updated internal modules/tests
  • refactored website.data_explorer to use HTMX components for all table entries, moving UI-specific features from DatabaseTable and HTMLMixin into DynamicTableForm
  • refactored the chemspace app to use an independent ChemspaceClient for source data management and chunked yielding, aligning its architecture with the chembl app
  • moved chemspace.utils.download_raw_files into ChemspaceClient.download_source_data
  • switched from ChemDoodle to Ketcher as the default molecule sketcher
  • updated scheduler to submit tasks as WorkItems instead of running them in-thread
  • removed unused web templates and static assets
  • updated envs for helm and docker-compose, where k3s is the top candidate for public production setups
  • renamed the base component from DynamicTableForm to TableComponent and moved it to simmate.website.data_explorer.components. Standardized all app components
  • cleaned up simmate.dockerfile by separating blender install and minimizing deps. Image is now <500mb
  • rebuilt molecule datastore class
  • adjusted s3 and datastore utils
  • optimized chemspace repartitioning
  • updated fingerprinting featurizers
  • refactored staged workflows, docker builds, and gh ci
  • updated chemspace s3 client
  • updated chemspace datastore

Fixes

  • patched connection contexts and closing in the database.external_connectors module
  • fixed htmx_molecule_input for non-chemdraw sketcher
  • fixed extra $$$$ delimiter being written on bulk sdf export
  • fixed typo in volume_change formula for relaxations
  • patched data explorer entries context
  • patched htmx forms and reports
  • updated dask requirement to <2026.3.1
  • bumped versions of various github actions in CI
  • patched status tracking logic
  • fixed project management mixin
  • added missing CAS migration